Talk:Commonly used strains
In the attached figure I show several tracks of sequencing data aligned to Ensembl R64.1.100.
Here you can see Illumina short-read WGS of FY4 (DGY1, grey track) showing an undocumented gene deletion. The gene is SRD1 (YCR018C), SRD1p has a role in pre-rRNA processing and is stress associated. This deletion isn't specific to our strain but seems to be present in the FY4 stock as I found it in other labs FY4 data as well (https://doi.org/10.1093/molbev/msaa172) , ('ANC', red track).
Using long-read sequencing of DGY1657 (https://doi.org/10.1371/journal.pbio.3000069) a FY4 derived strain (DGY1657, light blue track) we find evidence of a transposon (potentially, YJR027W) intervening in the region. Using RNAseq data of DGY1657 (blue track) we find that the remaining SRD1 region is being transcribed, but in the opposite direction (presumably from the bidirectional firing from the flanking CWH43 promoter). These transcripts do seem to recruit ribosomes (RPF, dark blue track) that initiate at a short ORF before presumably triggering NMD.
--Pieter Spealman 17:14, 19 October 2021 (PDT)